Browsing by Subject "antimicrobial resistance"

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  • Horesh, Gal; Blackwell, Grace A.; Tonkin-Hill, Gerry; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R. (2021)
    Escherichia coli is a highly diverse organism that includes a range of commensal and pathogenic variants found across a range of niches and worldwide. In addition to causing severe intestinal and extraintestinal disease, E. coli is considered a priority pathogen due to high levels of observed drug resistance. The diversity in the E. coli population is driven by high genome plasticity and a very large gene pool. All these have made E. coli one of the most well- studied organisms, as well as a commonly used laboratory strain. Today, there are thousands of sequenced E. coli genomes stored in public databases. While data is widely available, accessing the information in order to perform analyses can still be a challenge. Collecting relevant available data requires accessing different sources, where data may be stored in a range of formats, and often requires further manipulation and processing to apply various analyses and extract useful information. In this study, we collated and intensely curated a collection of over 10 000 E. coli and Shigella genomes to provide a single, uniform, high- quality dataset. Shigella were included as they are considered specialized pathovars of E. coli. We provide these data in a number of easily accessible formats that can be used as the foundation for future studies addressing the biological differences between E. coli lineages and the distribution and flow of genes in the E. coli population at a high resolution. The analysis we present emphasizes our lack of understanding of the true diversity of the E. coli species, and the biased nature of our current understanding of the genetic diversity of such a key pathogen.
  • Tiedje, James M.; Wang , Fang; Manaia, Celia M.; Virta, Marko; Sheng, Hongjie; Ma, Liping; Zhang , Tong; Topp, Edward (2019)
    Antibiotic resistance and its environmental component are gaining more attention as part of combating the growing healthcare crisis. The One Health framework, promulgated by many global health agencies, recognizes that antimicrobial resistance is a truly inter-domain problem in which human health, animal agriculture, and the environment are the core and interrelated components. This prospectus presents the status and issues relevant to the environmental component of antibiotic resistance, namely, the needs for advancing surveillance methodology: the environmental reservoirs and sources of resistance, namely, urban wastewater treatment plants, aquaculture production systems, soil receiving manure and biosolid, and the atmosphere which includes longer range dispersal. Recently, much work has been done describing antibiotic resistance genes in various environments; now quantitative, mechanistic, and hypothesis-driven studies are needed to identify practices that reduce real risks and maintain the effectiveness of our current antibiotics as long as possible. Advanced deployable detection methods for antibiotic resistance in diverse environmental samples are needed in order to provide the surveillance information to identify risks and define barriers that can reduce risks. Also needed are practices that reduce antibiotic use and thereby reduce selection for resistance, as well as practices that limit the dispersal of or destroy antibiotic-resistant bacteria or their resistance genes that are feasible for these varied environmental domains.
  • Hiltunen, Teppo; Virta, Marko; Laine, Anna-Liisa (2017)
    The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently. This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.
  • Wysok, Beata; Wojtacka, Joanna; Hänninen, Marja-Liisa; Kivistö, Rauni (2020)
    Campylobacteriosis is one of the most common causes of bacterial gastroenteritis. However, the clinical course of the illness varies in symptoms and severity. The aim of this study was to characterizeCampylobacter jejuni(34 isolates) andC. coli(9 isolates) from persons with diarrheal and non-diarrheal stools at the time of examination and fecal sampling, in Poland by using whole-genome sequencing (WGS). Multilocus sequence typing (MLST) analysis revealed a high diversity with a total of 20 sequence types (STs) among 26Campylobacterisolates from diarrheic and 13 STs among 17 isolates from non-diarrheic persons. ST-50 and ST-257 were most common in both groups. The phenotypic resistance rate was 74.4% for ciprofloxacin, 67.4% for sulfamethoxazole/trimethoprim, 58.1% for amoxicillin, 48.8% for tetracycline, and 46.5% for ceftriaxone. Only single isolates were resistant to erythromycin, gentamicin, and amoxicillin/clavulanic acid. Overall genotypic resistance toward amoxicillin, fluoroquinolones, tetracyclines, and aminoglycosides was predicted to occur in 93.1, 67.4, 48.8, and 11.6% of the isolates, respectively. None of the isolates showed the presence of theerm(B) gene or mutation in 23S rRNA. Neither was variation found in the important target region in L4 and L22 ribosomal proteins. In regard to the CmeABC efflux pump, a set of variable mutations affecting the regulatory region was noted. AllCampylobacterisolates possessed genes associated with adhesion (cadF,jlpA,porA, andpebA) and invasion (ciaB,pldA, andflaC). The type IV secretion system (T4SS) was found in isolates from both diarrheic (15.4%, CI 95%: 6.1-33.5%) and non-diarrheic (23.5%, CI 95%: 9.6-47.3%) persons. The rates of the presence of cytolethal distending toxincdtABCgene cluster and type VI secretion system (T6SS) were higher inCampylobacterisolates obtained from persons with diarrhea (96.2%, CI 95%: 81.7-99.3% and 26.9%, CI 95%: 13.7-46.1%) compared to isolates from non-diarrheic persons (76.5%, CI 95%: 52.7-90.4% and 11.8%, CI 95%: 3.3-34.3%). The lack of statistically significant differences between two groups in tested virulence factors suggests that individual susceptibility of the host might play more determining role in the disease outcome than characteristics of the infecting strain.
  • Sali, Virpi Tuulikki; Nykäsenoja, Suvi; Heikinheimo, Annamari; Hälli, Outi; Tirkkonen, Taneli; Heinonen, Mari (2021)
    In pigs, antimicrobial use (AMU) practices vary at different production phases between herds and between countries. Antimicrobial resistance (AMR) development is linked to AMU but recognized as a multi-factorial issue, and thus, any information increasing knowledge of AMU and AMR relationships is valuable. We described AMU and screened the carriage of different AMR phenotypes of indicator Escherichia coli in 25 selected Finnish piglet-producing and finishing herds that formed nine birth-to-slaughter production lines. Moreover, we studied associations between AMU and AMR in both herd types and throughout the production line. Treatment records were obtained from the national Sikava register for 1year, and AMU was quantified as mg/PCU (population correction unit) and TIs (treatment incidences). For phenotypic antimicrobial susceptibility testing, ten pen-level pooled feces samples (n=250) in each herd were collected from one room representing the oldest weaned piglets or the oldest finishing pigs. Majority of the medications (96.8%) was administered parenterally, and penicillin was the predominant antimicrobial in every herd. More different antimicrobial substances were used in piglet-producing than in finishing herds (median 5 and 1, respectively, p
  • Rouvinen, Vilma-Riitta (Helsingfors universitet, 2010)
    Psychrotrophs, which are mostly gram negative bacteria, can produce heat stable proteases and lipases. Even though these bacteria cannot survive pasteurization of milk, the enzymes can. This can cause problems for the dairy industry. Psychrotrophic milk isolates also have multidrug-resistant traits for antimicrobials and may act as reservoir for resistance genes. The aims of the study were to test denaturing gradient gel electrophoresis (DGGE) for PCR products obtained from organic and conventional raw milk bacteria, to optimize DNA-extraction protocols and PCR-conditions for the raw milk samples and study the bacterial population changes during the cold storage. The aim was also to study the antimicrobial susceptibility of the bacterial isolates. The DNA was extracted from the raw milk samples, when received and after 4 days cold storage, using commercial kits. Nested-PCR was performed and samples were analysed using DGGE. Susceptibility to antimicrobials was determined by growing bacteria on plates that contained two different concentrations of five antibiotics. From the five antibiotics two were used as a combination. The composition of the bacterial population changed during the cold (4ºC) storage: the difference in DGGE profiles was clear between 0 and 4 days cold storage. Fingerprint profile analysis showed that irrespective of the origin of the raw milk, the sample profiles were clustered according to the sampling date (day 0 or day 4). There was no clear difference between DGGE-profiles from conventional and organic milk. Proportion of psychrotrophic bacteria increased and antimicrobial resistance seemed to be more prevailing in conventional than in organic raw milk. Antimicrobial resistance decreased after four days storage at 4ºC, in most of the cases. We showed that the PCR-DGGE-method is an efficient tool to analyse the changes in bacterial populations in raw milk and that cold storage has an evident effect in population composition.
  • Pinto de Magalhães, Joana; Franko, Nina; Raboni, Samanta; Annunziato, Giannamaria; Tammela, Päivi; Bruno, Agostino; Bettati, Stefano; Armao, Stefano; Spadini, Costanza; Cabassi, Clotilde Silvia; Mozzarelli, Andrea; Pieroni, Marco; Campanini, Barbara; Costantino, Gabriele (2021)
    Many bacteria and actinomycetales use L-cysteine biosynthesis to increase their tolerance to antibacterial treatment and establish a long-lasting infection. In turn, this might lead to the onset of antimicrobial resistance that currently represents one of the most menacing threats to public health worldwide. The biosynthetic machinery required to synthesise L-cysteine is absent in mammals; therefore, its exploitation as a drug target is particularly promising. In this article, we report a series of inhibitors of Salmonella thyphimurium serine acetyltransferase (SAT), the enzyme that catalyzes the rate-limiting step of L-cysteine biosynthesis. The development of such inhibitors started with the virtual screening of an in-house library of compounds that led to the selection of seven structurally unrelated hit derivatives. A set of molecules structurally related to hit compound 5, coming either from the original library or from medicinal chemistry efforts, were tested to determine a preliminary structure-activity relationship and, especially, to improve the inhibitory potency of the derivatives, that was indeed ameliorated by several folds compared to hit compound 5 Despite these progresses, at this stage, the most promising compound failed to interfere with bacterial growth when tested on a Gram-negative model organism, anticipating the need for further research efforts.
  • Finnish Food Authority; Finnish Medicines Agency Fimea; University of Helsinki (Finnish Food Authority, 2019)
    Finnish Food Authority publications 6/2019
    Consumption of veterinary antimicrobials in food-producing animal species in Finland is low and in recent years, has decreased further. Drop is noted in sales of almost all antimicrobial classes. Particularly sales of orally administered products have decreased. Sales of tablets intended to companion animals has almost halved during this decade. Majority, two thirds, of all antimicrobial products sold in 2018 was for treatment of individual animals and the remaining third products applicable for group treatment. Narrow spectrum penicillin G was the most used antimicrobial for animals and the proportion of highest priority critically important antimicrobials (HPCIA) was very low. The antimicrobial resistance situation in bacteria from animals and food has remained relatively good in Finland. However, in certain bacteria resistance was detected in moderate or high levels. Therefore, there is a need to further emphasise the preventive measures and prudent use of antimicrobials. It is important to follow the Finnish recommendations for the use of antimicrobials in animals. Among salmonella and campylobacter isolated from Finnish food-producing animals, resistance levels were mainly low. For the first time in Finland, multidrug resistant S. Kentucky was isolated from cattle in 2018. From 2014, the occurrence of fluoroquinolone and tetracycline resistance in campylobacter from broilers have varied. The occurrence of fluoroquinolone resistance in indicator E. coli has increased although the resistance is still low. Among pathogenic bacteria isolated from food-producing animals the most notifiable change was the worsening of resistance in some bovine respiratory disease pathogens. In other pathogens from food-producing animals the resistance situation remained similar as in previous years. The proportion of resistant bacterial isolates from companion animals and horses decreased for nearly all antimicrobials. However, the proportion of resistant isolates is still high for some antimicrobials. ESBL/AmpC-producing bacteria were still encountered in broilers and broiler meat; prevalence of these bacteria in broiler meat was somewhat lower in 2018 compared to 2016.
  • Finnish Food Authority; Finnish Medicines Agency Fimea; University of Helsinki (Finnish Food Authority, 2020)
    Finnish Food Authority publications 5/2020
    Sales of veterinary antimicrobials in food-producing animal species in Finland remained low although it increased slightly in 2019. Majority, almost two thirds, of all antimicrobial products are given to individual animals, and products intended for group treatment accounted for just over a third. Injectable penicillin is still the most commonly used antimicrobial. The next most common agents are orally administered tetracyclines and orally administered sulfonamide-trimethoprim combination, both of which saw a clear increase in sales last year. Sales of reserve antimicrobials (HPCIA, WHO list) for the treatment of animals remained very low also in 2019. The antimicrobial resistance situation in bacteria from animals and food has remained relatively good in Finland. However, in certain bacterial species resistance was detected in moderate or high levels. Therefore, there is a need to further emphasise the preventive measures and prudent use of antimicrobials. It is important to follow the Finnish recommendations for the use of antimicrobials in animals. Among salmonella and campylobacter from Finnish food-producing animals, resistance levels were mainly low. For the first time in Finland, multidrug resistant monophasic Salmonella Typhimurium was isolated from a few cattle and pig farms in 2019. From 2014 onwards, the occurrence of fluoroquinolone and tetracycline resistant campylobacter from broilers have varied. No significant changes have been observed in the occurrence of resistant indicator E. coli from pigs except for tetracycline resistance which has decreased since 2013. The resistance situation among pathogenic bacteria isolated from food-producing animals was similar as in previous year. Resistant isolates are still detected most commonly among enterotoxigenic E. coli from pigs. The proportion of resistant bacterial isolates from companion animals and horses decreased for nearly all antimicrobials. However, resistance against some antimicrobials increased for certain bacterial species. The prevalence of ESBL/AmpC-producing bacteria in slaughtered pigs as well as in pork and beef was low or non-existent.
  • Townsend, Eleanor M; Kelly, Lucy; Gannon, Lucy; Muscatt, George; Dunstan, Rhys; Michniewski, Slawomir; Sapkota, Hari; Kiljunen, Saija J; Kolsi, Anna; Skurnik, Mikael; Lithgow, Trevor; Millard, Andrew D; Jameson, Eleanor (2021)
    Introduction: Klebsiella is a clinically important pathogen causing a variety of antimicrobial resistant infections in both community and nosocomial settings, particularly pneumonia, urinary tract infection, and sepsis. Bacteriophage (phage) therapy is being considered a primary option for the treatment of drug-resistant infections of these types. Methods: We report the successful isolation and characterization of 30 novel, genetically diverse Klebsiella phages. Results: The isolated phages span six different phage families and nine genera, representing both lysogenic and lytic lifestyles. Individual Klebsiella phage isolates infected up to 11 of the 18 Klebsiella capsule types tested, and all 18 capsule-types were infected by at least one of the phages. Conclusions: Of the Klebsiella-infecting phages presented in this study, the lytic phages are most suitable for phage therapy, based on their broad host range, high virulence, short lysis period and given that they encode no known toxin or antimicrobial resistance genes. Phage isolates belonging to the Sugarlandvirus and Slopekvirus genera were deemed most suitable for phage therapy based on our characterization. Importantly, when applied alone, none of the characterized phages were able to suppress the growth of Klebsiella for more than 12 h, likely due to the inherent ease of Klebsiella to generate spontaneous phage-resistant mutants. This indicates that for successful phage therapy, a cocktail of multiple phages would be necessary to treat Klebsiella infections.
  • Benkwitz-Bedford, Sam; Palm, Martin; Demirtas, Talip Yasir; Mustonen, Ville; Farewell, Anne; Warringer, Jonas; Parts, Leopold; Moradigaravand, Danesh (2021)
    Escherichia coli is an important cause of bacterial infections worldwide, with multidrug-resistant strains incurring substantial costs on human lives. Besides therapeutic concentrations of antimicrobials in health care settings, the presence of subinhibitory antimicrobial residues in the environment and in clinics selects for antimicrobial resistance (AMR), but the underlying genetic repertoire is less well understood. Here, we used machine learning to predict the population doubling time and cell growth yield of 1,407 genetically diverse E. coli strains expanding under exposure to three subinhibitory concentrations of six classes of antimicrobials from single-nucleotide genetic variants, accessory gene variation, and the presence of known AMR genes. We predicted cell growth yields in the held-out test data with an average correlation (Spearman's rho) of 0.63 (0.36 to 0.81 across concentrations) and cell doubling times with an average correlation of 0.59 (0.32 to 0.92 across concentrations), with moderate increases in sample size unlikely to improve predictions further. This finding points to the remaining missing heritability of growth under antimicrobial exposure being explained by effects that are too rare or weak to be captured unless sample size is dramatically increased, or by effects other than those conferred by the presence of individual single-nucleotide polymorphisms (SNPs) and genes. Predictions based on whole-genome information were generally superior to those based only on known AMR genes and were accurate for AMR resistance at therapeutic concentrations. We pinpointed genes and SNPs determining the predicted growth and thereby recapitulated many known AMR determinants. Finally, we estimated the effect sizes of resistance genes across the entire collection of strains, disclosing the growth effects for known resistance genes in each individual strain. Our results underscore the potential of predictive modeling of growth patterns from genomic data under subinhibitory concentrations of antimicrobials, although the remaining missing heritability poses a challenge for achieving the accuracy and precision required for clinical use. IMPORTANCE Predicting bacterial growth from genome sequences is important for a rapid characterization of strains in clinical diagnostics and to disclose candidate novel targets for anti-infective drugs. Previous studies have dissected the relationship between bacterial growth and genotype in mutant libraries for laboratory strains, yet no study so far has examined the predictive power of genome sequence in natural strains. In this study, we used a high-throughput phenotypic assay to measure the growth of a systematic collection of natural Escherichia coli strains and then employed machine learning models to predict bacterial growth from genomic data under nontherapeutic subinhibitory concentrations of antimicrobials that are common in nonclinical settings. We found a moderate to strong correlation between predicted and actual values for the different collected data sets. Moreover, we observed that the known resistance genes are still effective at sublethal concentrations, pointing to clinical implications of these concentrations.
  • Castro, Hanna; Douillard, Francois; Korkeala, Hannu; Lindström, Miia (2021)
    Listeria monocytogenes is a foodborne pathogen and a resilient environmental saprophyte. Dairy farms are a reservoir of L. monocytogenes, and strains can persist on farms for years. Here, we sequenced the genomes of 250 L. monocytogenes isolates to investigate the persistence and mobile genetic elements (MGEs) of Listeria strains inhabiting dairy farms. We performed a single-nucleotide polymorphism (SNP)-based phylogenomic analysis to identify 14 monophyletic clades of L. monocytogenes persistent on the farms for ≥6 months. We found that prophages and other mobile genetic elements were, on average, more numerous among isolates in persistent than nonpersistent clades, and we demonstrated that resistance genes against bacitracin, arsenic, and cadmium were significantly more prevalent among isolates in persistent than nonpersistent clades. We identified a diversity of mobile elements among the 250 farm isolates, including three novel plasmids, three novel transposons, and a novel prophage harboring cadmium resistance genes. Several of the mobile elements we identified in Listeria were identical to the mobile elements of enterococci, which is indicative of recent transfer between these genera. Through a genome-wide association study, we discovered that three putative defense systems against invading prophages and plasmids were negatively associated with persistence on farms. Our findings suggest that mobile elements support the persistence of L. monocytogenes on dairy farms and that L. monocytogenes inhabiting the agroecosystem is a potential reservoir of mobile elements that may spread to the food industry. IMPORTANCE Animal-derived raw materials are an important source of L. monocytogenes in the food industry. Knowledge of the factors contributing to the pathogen's transmission and persistence on farms is essential for designing effective strategies against the spread of the pathogen from farm to fork. An increasing body of evidence suggests that mobile genetic elements support the adaptation and persistence of L. monocytogenes in the food industry, as these elements contribute to the dissemination of genes encoding favorable phenotypes, such as resilience against biocides. Understanding of the role of farms as a potential reservoir of these elements is needed for managing the transmission of mobile elements across the food chain. Because L. monocytogenes coinhabits the farm ecosystem with a diversity of other bacterial species, it is important to assess the degree to which genetic elements are exchanged between Listeria and other species, as such exchanges may contribute to the rise of novel resistance phenotypes.
  • Kurittu, Paula; Khakipoor, Banafsheh; Aarnio, Maria; Nykäsenoja, Suvi; Brouwer, Michael; Myllyniemi, Anna-Liisa; Vatunen, Elina; Heikinheimo, Annamari (2021)
    Plasmid-mediated extended-spectrum beta-lactamase (ESBL), AmpC, and carbapenemase producing Enterobacteriaceae, in particular Escherichia coli and Klebsiella pneumoniae, with potential zoonotic transmission routes, are one of the greatest threats to global health. The aim of this study was to investigate global food products as potential vehicles for ESBL/AmpC-producing bacteria and identify plasmids harboring resistance genes. We sampled 200 food products purchased from Finland capital region during fall 2018. Products originated from 35 countries from six continents and represented four food categories: vegetables (n = 60), fruits and berries (n = 50), meat (n = 60), and seafood (n = 30). Additionally, subsamples (n = 40) were taken from broiler meat. Samples were screened for ESBL/AmpC-producing Enterobacteriaceae and whole genome sequenced to identify resistance and virulence genes and sequence types (STs). To accurately identify plasmids harboring resistance and virulence genes, a hybrid sequence analysis combining long- and short-read sequencing was employed. Sequences were compared to previously published plasmids to identify potential epidemic plasmid types. Altogether, 14 out of 200 samples were positive for ESBL/AmpC-producing E. coli and/or K. pneumoniae. Positive samples were recovered from meat (18%; 11/60) and vegetables (5%; 3/60) but were not found from seafood or fruit. ESBL/AmpC-producing E. coli and/or K. pneumoniae was found in 90% (36/40) of broiler meat subsamples. Whole genome sequencing of selected isolates (n = 21) revealed a wide collection of STs, plasmid replicons, and genes conferring multidrug resistance. bla(CTX-M-15)-producing K. pneumoniae ST307 was identified in vegetable (n = 1) and meat (n = 1) samples. Successful IncFII plasmid type was recovered from vegetable and both IncFII and IncI1-I gamma types from meat samples. Hybrid sequence analysis also revealed chromosomally located beta-lactamase genes in two of the isolates and indicated similarity of food-derived plasmids to other livestock-associated sources and also to plasmids obtained from human clinical samples from various countries, such as IncI type plasmid harboring bla(TEM-52C) from a human urine sample obtained in the Netherlands which was highly similar to a plasmid obtained from broiler meat in this study. Results indicate certain foods contain bacteria with multidrug resistance and pose a possible risk to public health, emphasizing the importance of surveillance and the need for further studies on epidemiology of epidemic plasmids.
  • Kovanen, Sara; Rossi, Mirko; Pohja-Mykrä, Mari; Nieminen, Timo; Raunio-Saarnisto, Mirja; Sauvala, Mikaela; Fredriksson-Ahomaa, Maria; Hänninen, Marja-Liisa; Kivistö, Rauni Inari (2019)
    Poultry are considered a major reservoir and source of human campylobacteriosis, but the roles of environmental reservoirs, including wild birds, have not been assessed in depth. In this study, we isolated and characterized Campylobacter jejuni from western jackdaws (n = 91, 43%), mallard ducks (n = 82, 76%), and pheasants (n = 9, 9%). Most of the western jackdaw and mallard duck C. jejuni isolates represented multilocus sequence typing (MLST) sequence types (STs) that diverged from those previously isolated from human patients and various animal species, whereas all pheasant isolates represented ST-19, a common ST among human patients and other hosts worldwide. Whole-genome MLST revealed that mallard duck ST-2314 and pheasant ST-19 isolates represented bacterial clones that were genetically highly similar to human isolates detected previously. Further analyses revealed that in addition to a divergent ClonalFrame genealogy, certain genomic characteristics of the western jackdaw C. jejuni isolates, e.g., a novel cdtABC gene cluster and the type VI secretion system (T6SS), may affect their host specificity and virulence. Game birds may thus pose a risk for acquiring campylobacteriosis; therefore, hygienic measures during slaughter and meat handling warrant special attention. IMPORTANCE The roles of environmental reservoirs, including wild birds, in the molecular epidemiology of Campylobacter jejuni have not been assessed in depth. Our results showed that game birds may pose a risk for acquiring campylobacteriosis, because they had C. jejuni genomotypes highly similar to human isolates detected previously. Therefore, hygienic measures during slaughter and meat handling warrant special attention. On the contrary, a unique phylogeny was revealed for the western jackdaw isolates, and certain genomic characteristics identified among these isolates are hypothesized to affect their host specificity and virulence. Comparative genomics within sequence types (STs), using whole-genome multilocus sequence typing (wgMLST), and phylogenomics are efficient methods to analyze the genomic relationships of C. jejuni isolates.
  • Hinchliffe, Steve; Butcher, Andrea; Rahman, Muhammad Meezanur; Guilder, James; Tyler, Charles; Verner-Jeffries, David (2021)
    Improved biosecurity and livestock disease control measures in low resource settings are often regarded as beneficial for agricultural productivity, rural incomes, global health, and sustainability. In this paper we present data from a study of shrimp and prawn aquaculture in Bangladesh to argue that this relationship is not as straightforward as it would seem. Analysing quantitative and qualitative data from a multi‐method field study involving 300 “missing middle” farmers, we demonstrate the importance of socio‐economic and ecological conditions to any disease management strategy. We describe how a technical programme to introduce “disease‐free” seed faltered partly as a result of the farmers' tendency to offset disease and livelihood risks by frequently re‐stocking their ponds. Changes to seed provision were accompanied by calls to alter farmers' livestock production practices. Paradoxically, these changes exposed farmers to more intense risks, potentially locking them into unsustainable disease management practices. The analysis emphasises that vernacular farming practices should be considered as key assets rather than barriers to disease management strategies, and that closer attention be paid to value chain and other risks as drivers of unsustainable practices.
  • Turunen, Katri A.; Kantele, Anu (2021)
    Background As antimicrobials increase the risk of acquiring multidrug-resistant (MDR) bacteria, unnecessary antibiotics should be avoided for travellers’ diarrhoea (TD). Antibiotics are recommended in TD accompanied by fever or incapacitation (TD justifying use of antibiotics, TDjuAB). Seeking tools for reducing antibiotic use, we explored factors predisposing to TDjuAB and scrutinized antibiotic treatment among those with TDjuAB [TDjuAB(+) subgroup] and those with diarrhoea not justifying antibiotics [TDjuAB(−) subgroup]. Methods We conducted a study among 370 prospectively recruited visitors to the tropics. Stool samples and questionnaires were collected before and after travel. Enteric pathogens were analysed by qPCR for enteropathogenic (EPEC), enteroaggregative (EAEC), enterotoxigenic (ETEC), enterohaemorrhagic (EHEC) and enteroinvasive (EIEC) E. coli/Shigella, Campylobacter, Salmonella, Yersinia and Vibrio cholerae, and for ETEC’s toxins LT (heat-labile), STh (human heat-stable) and STp (porcine heat-stable). TD was defined by the WHO criteria and TDjuAB as diarrhoea accompanied by fever, and/or disrupting or preventing daily activities. Multivariable analysis was applied—separately for travel-related factors and pathogens—to identify risk factors for TDjuAB(+). Results Among the 370 travellers, TD was contracted by 253 (68%), categorized as TDjuAB(+) in 93/253 (37%) and TDjuAB(−) in 160/253 (63%) of the cases. Antibiotics were used for TD by 41% in TDjuAB(+) and by 7% in the TDjuAB(−) group. Relative risk ratios (RRR)s are presented for both the TDjuAB(+) and the TDjuAB(−) groups. TDjuAB(+) was associated with long travel duration and young age. Among the 298 subjects not having taken antibiotics, increased RRRs were found e.g. for findings of Campylobacter coli/jejuni and ETEC’s STh toxin. Conclusions The first to analyse risk factors for TDjuAB, our study presents RRRs for demographic and behavioural factors and for various pathogens. Only less than half of those in the TDjuAB(+) group took antibiotics, which demonstrates that most cases meeting the current criteria recover without antimicrobial treatment.
  • Karnola, Laura (Helsingin yliopisto, 2020)
    Antimicrobial resistance (AMR) is an emerging global health threat with the growing number of antibiotic-resistant bacteria (ARB) having the alarming potential to return humanity to the pre-antibiotic era. Intensive animal production is globally one of the biggest sectors using antibiotics. It has been studied that fertilizing fields with animal manure spreads antimicrobial resistance genes (ARGs) in natural environments. The aim of this study was to determine the host range of three ARGs tetM, strB and qacE∆1 in soil and manure samples collected from a Finnish swine farm. In addition, the microbial communities in the same soil and manure samples were studied and compared. Six different sample types were taken, four from soil and two from manure. Soil samples included unfertilized soil, fertilized soil, soil two weeks after fertilization and soil six weeks after fertilization. Manure samples were taken from fresh and stored manure. Host range analysis was done by using Emulsion, Paired Isolation and Concatenation PCR (epicPCR). EpicPCR enables to link a gene of interest to the 16S rRNA gene of the bacterium that carries the gene in its genome. Microbial communities in soil and manure were analyzed and compared with the traditional 16S rRNA gene sequencing. Host range analysis with epicPCR revealed various bacterial genera as carriers for studied ARGs. Fertilized soil had the highest number of genera carrying the ARGs. This indicates that land application with animal manure increases the ARG load in soil. Microbial communities were found significantly different in soil and manure according to the 16S rRNA gene sequences. The results of epicPCR indicate that epicPCR has also potential for solid samples such as soil and manure as according to publications it has been mainly used for different water samples e.g., wastewaters. As a method epicPCR still requires optimization if applied for these sample materials in the future. A clear reduction in the number of genera carrying the ARGs was observed in six weeks after fertilization. Therefore, fertilizing fields only before cropping season, instead of fertilizing the fields year-round, might be one solution for reducing the ARG dissemination in soil in countries with high antibiotic consumption.
  • Thomson, Katariina; Aaltonen, Hanna (Maa- ja metsätalousministeriö, 2019)
    Publications of the Ministry of Agriculture and Forestry
    This guide has been drafted as a concrete protocol of the National Action Plan on Antimicrobial Resistance in order to provide practical assistance for the development of hygiene practices at veterinary receptions and prevent the spread of antimicrobial resistance. Increasing antimicrobial resistance is one of the biggest national health threats in the world. The antimicrobial resistance of pathogenic bacteria in animals is also increasing at an alarming rate. Reducing the use of antimicrobials mitigates the development of resistance and improving the level of hygiene at veterinary receptions can also effectively prevent infections and the spread of antimicrobial resistance. Daily hygiene procedures and taking standard precautions form the basis for preventing infections. These precautions must be taken with each and every patient by all reception personnel. Proper hand hygiene is the foundation of hygiene protocols. In addition to proper hand hygiene, hygiene protocols and standard precautions include aseptic technique, the proper use of personal protection equipment, the immediate cleaning of secretions, the prevention of needle stick and cutting injuries, and maintaining reception tidiness and cleanliness. Furthermore, special attention must be given to the treatment and handling of risk patients, i.e. potential carriers of resistant bacteria and animals with contagious diseases. The identification of risk patients, choosing the right treatment room and treatment planning at the reception are crucial to avoiding contamination of the facility and the spread of infection transmitted by the hands of personnel, the environment and the equipment used. This guide will help point out essential factors in the planning of hygiene protocols at different veterinary receptions.